Contacts of the helix formed by residues 100 - 108 (chain B) in PDB entry 2FI2
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with ILE 100 (chain B).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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52A TYR* 4.1 13.5 - - + +
54A GLU* 4.7 12.1 - - + +
96B LEU* 3.7 10.5 - - + -
97B PRO* 3.0 34.5 + - + -
99B GLU* 1.3 82.4 - - + +
101B GLN* 1.3 65.9 + - - +
103B ARG* 3.1 14.6 + - - +
104B VAL* 3.2 13.0 + - - +
119B VAL* 3.3 31.6 - - + -
122B LEU* 3.7 35.6 - - + +
123B ARG* 4.8 3.1 - - - +
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Residues in contact with GLN 101 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B LEU* 2.9 27.6 + - - +
94B GLY* 3.3 17.6 + - - -
96B LEU* 3.2 27.2 + - + +
97B PRO 2.7 20.1 + - - +
98B PRO* 3.8 8.0 - - - +
100B ILE* 1.3 74.6 - - - +
102B ALA* 1.3 55.4 + - - +
104B VAL* 3.1 2.1 + - - +
105B GLN* 2.7 52.3 + - + +
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Residues in contact with ALA 102 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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98B PRO 2.9 19.7 + - - +
99B GLU* 3.5 8.7 - - - +
100B ILE 3.2 0.2 - - - -
101B GLN* 1.3 76.0 - - - +
103B ARG* 1.3 58.5 + - + +
105B GLN* 3.4 6.9 + - - +
106B GLY* 2.8 27.5 + - - -
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Residues in contact with ARG 103 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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99B GLU* 3.4 15.8 + - - +
100B ILE* 3.1 9.3 + - - +
102B ALA* 1.3 78.5 - - - +
104B VAL* 1.3 62.2 + - - +
106B GLY* 3.4 7.9 + - - -
107B GLN* 3.4 22.4 - - - +
118B LEU* 5.4 1.1 - - - -
122B LEU* 3.4 31.6 - - + +
127B GLY* 6.2 1.6 - - - -
128B GLY 4.1 21.1 + - - +
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Residues in contact with VAL 104 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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93B LEU* 3.6 29.4 - - + -
96B LEU* 3.7 21.1 - - + -
100B ILE 3.2 12.8 + - - +
101B GLN 3.1 6.5 + - - +
103B ARG* 1.3 77.9 - - - +
105B GLN* 1.3 57.3 + - - +
107B GLN* 2.8 5.5 + - - +
108B ARG* 2.7 32.8 + - - -
109B PRO* 3.4 27.6 - - + -
115B ALA 4.6 1.3 - - - +
118B LEU* 4.0 17.9 - - + -
119B VAL* 3.7 15.5 - - + -
122B LEU* 5.1 0.7 - - + -
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Residues in contact with GLN 105 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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44B ARG* 3.9 4.3 + - - -
93B LEU* 3.4 25.6 - - - +
101B GLN* 2.7 56.5 + - + +
102B ALA* 3.9 8.7 - - - +
104B VAL* 1.3 86.4 - - - +
106B GLY* 1.3 59.9 + - - +
107B GLN 3.1 1.1 + - - -
108B ARG* 3.0 61.9 + - - +
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Residues in contact with GLY 106 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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102B ALA 2.8 17.0 + - - -
103B ARG* 3.8 2.5 - - - -
104B VAL 3.1 1.0 - - - -
105B GLN* 1.3 76.4 - - - +
107B GLN* 1.3 64.2 + - - +
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Residues in contact with GLN 107 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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103B ARG* 3.4 13.7 + - - +
104B VAL 2.8 4.5 + - - +
105B GLN 3.1 0.2 - - - -
106B GLY* 1.3 83.0 - - - +
108B ARG* 1.3 76.4 + - - +
109B PRO* 5.9 0.2 - - + -
118B LEU* 3.4 38.8 - - + +
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Residues in contact with ARG 108 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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41B GLU* 5.5 11.4 - - + +
44B ARG* 4.0 7.0 - - - +
45B LEU* 3.3 49.2 - - + +
93B LEU* 6.1 0.4 - - - -
104B VAL* 2.7 14.1 + - - -
105B GLN* 3.0 63.3 + - - +
106B GLY 5.2 0.2 - - - -
107B GLN* 1.3 80.6 - - - +
109B PRO* 1.3 71.4 - - - +
110B GLY 3.6 1.6 - - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il